Results of PCR revealed that ART5 which is a closely linked marker in the promoter regionof SUB1C a transcription-factor gene (Sarkar and Bhattacharjee, 2011) showed bands insome of the genotypes while the presence of this marker was nullified in all the rest of thegenotypes used in this study. Like-wise, SC3 which is a closely linked marker with SUB1Ashowed polymorphism in other genotypes. Only few genotypes showed distinct bands in caseof both the markers. Therefore, concluding these results it may be suggested that both themarkers i.e. ART5 and SC3 may be used as potential PCR-based markers for molecularscreening of rice genotypes for SUB1 QTL (Sarkar and Bhattacharjee, 2011). Genotyping ofall the lines imported from IRRI confirmed the presence of SUB1gene.Furthermore, both theprimers did not show polymorphism in other local cultivars as well as exotic cultivars. The obtained results clearly indicated that all the genotypes with submergence tolerant gene(SUB1) showed significantly greater tolerance level as compared to other local cultivars/varieties, authenticating the effectiveness of SUB1QTL in conferring submergence tolerance(Akinwaleet al 2012).However, a significant variation was observed among the studiedcultivars in tolerance for submergence as well as all other traits studied. (a) Physical condition after treatment Irradiance due to turbidity and limited CO2 supply are two major factors for tissue deathin case of stagnant floodwater submergence. As a result of these factors, rice plantsbecome unable to photosynthesize and continue to maintain supply of carbohydrate forrespiration and alcoholic fermentation (Setter et al., 1997). Therefore, data for physicalcondition of the plants of each genotype were collected after submergence stress in termsof tissue death due to prolonged condition of submergence stress. Comparativelyhealthiest plants were given 5 ranking while the plants having poorest health conditionwere given 0 ranking and so on. Results clearly showed that genotypes without SUB1geneshowed highest rate of tissue death as compared to genotypes with SUB1gene.Furthermore, the SUB1genotypes also showed variation in expressivity of the SUB1gene.Five genotypes showed 5 ranking (very good) in physical condition after submergencestress, thirty one showed 4 (good), Nineteen showed 3 (fair) while the rest showed <3(below average and poor) ranking. Only five plants that maintained their health status andshowed very good health condition after de-submergence will be considered for beingused as donor parents (figure 1). (b) Plant survival percentage The data for plant survival percentage was collected 60 days after submergence treatmentwhen submergence susceptible checks had completely dried. Plant survival percentagevaried from 0% (all plants dried) to 100% (all plants were green after submergencetreatment) survival. Considering IR64-SUB1line (showing 90.6% survival) assubmergence tolerant while IR6, NSICRC-222 andSabitri (showing survival percentageof 21.9%, 18.8-21.9% and 9.4% respectively) as submergence susceptible lines, criterionfor evaluating the lines for submergence tolerance rice lines may be designed. It can beperceived from figure 2 that the entries showing above 80% survival percentage can bepresumed as submergence tolerant, while below 20% as submergence susceptible lines.Results indicated that all the studied lines with submergence tolerance gene (SUB1) hassignificant higher survival rate than other varieties under evaluation (Akinwaleet al 2012).All the local cultivars could not survive at all. (c) Submergence Tolerance Index Similarly, Submergence Tolerance Index (STI) was calculated in order to measure thelevel of tolerance to submergence stress. Submergence tolerant lines showed above 8.0index while the susceptible lines had less than 2.0 tolerance index value. IR64SUB1(IRRIvariety)showedSTIvalueof0.906indicatingthat it is a submergencetolerant line whereas IR6, NSICRS222 and Sabitri, with no SUB1 QTL showed STI valueof 0.219, 0.188 and 0.094 respectively. All the local approved varieties of Pakistan showed zero tolerance level as indicated by the lowest STI values. Further, the lines withSUB1QTL (submergence tolerant gene) showed significantly higher STI value ascompared to local cultivars deprive of the gene. It was further observed that there wasalso a significant variability among lines with SUB1gene. This reconfirms the previousfindings that the flood-tolerant SUB1 gene, when transferred into popular farmerpreferredrice varieties, enables them to survive even after two weeks of totalsubmergence (Xu et al., 2004; Mackill 2006).Radar graph (figure 3) shows theperformance of the genotypes under submerged condition of 14 days in terms ofTolerance Index Values from highest to lowest. It shows that IR64-SUB1 (Tolerancecheck) line earns 17th position with TI value of 0.906. Among all, 18 lines showed TIvalue above 0.90 (Highly tolerant), 13 lines more than 0.80 TI values (ModeratelyTolerant), 13 lines between 0.60 to 0.80 TI values (Moderately Susceptible) lines, andrest of the lines showed highly susceptible performance with TI values below 0.6.likewiseamong the susceptible checks (without SUB1gene), IR6 got the 85th position, bothNSICRC222 lines got 86th and 87th positions, both lines of Sabitri got 103rd and 104thposition. All the local cultivars poorly performed in submerged condition with TI valuesbelow 0.2 indicating that there is no tolerance to submergence and there is dire need totransfer SUB1QTL into our local high yielding cultivars in order to cope withgrowingfrequency of floods in imminent era.